Is there a difference between Italian come sei? and come stai?

It means the same thing, it means to ask you how you are doing, which is the same as how are you and how do you do in English, but with different verbs, one uses essere and the other stare, and the answer is the same. To say that you are doing well, you need to say "bene", which is usually "cosi", which is not good enough, which is "male".